2010 Prius p0a80 I Replaced the hybrid but still won't run on battery

Trying to explain this in as simple of a way as possible.

A few weeks ago my 2010 Prius (115k miles) had the error "Check Hybrid System". This came off the heels of the car stalling a few days before when accelerating from a stopped position. It had also been giving me trouble when accelerating and was giving a delayed response on more than one occasion. I looked into the manufactures recall I recently got in the mail and realized this problem was due to a software update. I did this and to play it safe, hoping for a less expensive fix, I replaced the 12v. After doing this the "Check Hybrid System" went away. (I assumed this was from unplugging the battery and this caused the error to erase) I continued to drive the Prius and pretended everything was ok. I hoped this was the problem. After driving the car for 3 weeks the same thing popped up "Check hybrid system" This time I took it in and was told the hybrid battery needed to be replaced. One thing I notice is the car had stopped running on the hybrid battery. At this point it wouldn't turn off as I sat at traffic lights and wouldn't run on the Hybrid when I was accelerating gently at low speeds. (or any other time it use to kick on)
I bought a hybrid battery and installed it just last night and I drove it around for 10 minutes. I noticed the "Check Hybrid System" was still on. Is this because the error code needs to be cleared?

Secondly I noticed the car still refused to run on electric. I don't know a lot about Prius' but my thought was when the Prius thinks that the hybrid battery is bad it automatically stops using the hybrid. Perhaps this is why my car showed the hybrid battery as fully charged after driving for about 10 minutes but still wouldn't use it. Could this be because the code is still registered in the car and some sort of smart fail safe system is keeping it from being used?

 

update: I detached the 12v battery for 30 minutes and after reattaching "check hybrid system" isn't displayed. It also starting running on hybrid battery power as soon as the car powered up. This is something it wouldn't do before. I wonder if this means there is something else that is a problem.